since V-REP 3.4.0, the graphs are displayed in custom UI windows. Until then, the graphs were displayed in floating windows, and you are not able to modify the position of a floating window. But by using simExtCustomUI_setPosition you should be able to change the position of the window.

For details, have a look at a scene that uses graphs (e.g. BarrettHandPickAndPlace.ttt) and inspect the customization script attached to object robot_robot_distance: it basically refers to a script in /lua/graph_customization.lua.